Starting phenix.real_space_refine on Mon Nov 18 17:02:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/11_2024/8t4m_41036.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/11_2024/8t4m_41036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/11_2024/8t4m_41036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/11_2024/8t4m_41036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/11_2024/8t4m_41036.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/11_2024/8t4m_41036.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 140 5.16 5 C 10984 2.51 5 N 2864 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4228 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 9.28, per 1000 atoms: 0.55 Number of scatterers: 17000 At special positions: 0 Unit cell: (112.288, 112.288, 128.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 4 15.00 O 3008 8.00 N 2864 7.00 C 10984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 2.5 seconds 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 73.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 264 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 289 Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP D 589 " --> pdb=" O THR D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU D 618 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 620 " --> pdb=" O ASN D 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 289 Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 439 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP C 589 " --> pdb=" O THR C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 289 Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU B 618 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 289 Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER D 204 " --> pdb=" O ASN D 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR D 524 " --> pdb=" O LYS D 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS D 528 " --> pdb=" O THR D 524 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR C 524 " --> pdb=" O LYS C 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER B 204 " --> pdb=" O ASN B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR B 524 " --> pdb=" O LYS B 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A 524 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5404 1.35 - 1.47: 4290 1.47 - 1.58: 7450 1.58 - 1.70: 8 1.70 - 1.82: 244 Bond restraints: 17396 Sorted by residual: bond pdb=" C3' CMP A 901 " pdb=" C4' CMP A 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP B 901 " pdb=" C4' CMP B 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" CA PRO D 577 " pdb=" C PRO D 577 " ideal model delta sigma weight residual 1.520 1.537 -0.018 1.42e-02 4.96e+03 1.52e+00 ... (remaining 17391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 23320 2.29 - 4.58: 188 4.58 - 6.87: 36 6.87 - 9.16: 12 9.16 - 11.45: 4 Bond angle restraints: 23560 Sorted by residual: angle pdb=" N ILE C 359 " pdb=" CA ILE C 359 " pdb=" C ILE C 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE D 359 " pdb=" CA ILE D 359 " pdb=" C ILE D 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CB MET A 215 " pdb=" CG MET A 215 " pdb=" SD MET A 215 " ideal model delta sigma weight residual 112.70 124.15 -11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 23555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 9800 26.04 - 52.07: 500 52.07 - 78.11: 52 78.11 - 104.14: 4 104.14 - 130.18: 4 Dihedral angle restraints: 10360 sinusoidal: 4084 harmonic: 6276 Sorted by residual: dihedral pdb=" CA ASP C 209 " pdb=" C ASP C 209 " pdb=" N PRO C 210 " pdb=" CA PRO C 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP B 209 " pdb=" C ASP B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N PRO A 210 " pdb=" CA PRO A 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 10357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1551 0.024 - 0.049: 581 0.049 - 0.073: 348 0.073 - 0.097: 84 0.097 - 0.122: 64 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE D 206 " pdb=" N ILE D 206 " pdb=" C ILE D 206 " pdb=" CB ILE D 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 2625 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 480 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO C 481 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 481 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 481 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 480 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO D 481 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 481 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 481 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 480 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO B 481 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " 0.024 5.00e-02 4.00e+02 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2200 2.75 - 3.29: 16867 3.29 - 3.83: 28535 3.83 - 4.36: 31712 4.36 - 4.90: 57736 Nonbonded interactions: 137050 Sorted by model distance: nonbonded pdb=" NZ LYS D 108 " pdb=" OE2 GLU C 436 " model vdw 2.217 3.120 nonbonded pdb=" OE2 GLU D 436 " pdb=" NZ LYS A 108 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS B 108 " pdb=" OE2 GLU A 436 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS C 108 " pdb=" OE2 GLU B 436 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR D 435 " pdb=" OE1 GLU A 452 " model vdw 2.240 3.040 ... (remaining 137045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 39.290 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17396 Z= 0.140 Angle : 0.565 11.451 23560 Z= 0.283 Chirality : 0.037 0.122 2628 Planarity : 0.003 0.044 2956 Dihedral : 14.873 130.178 6296 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2116 helix: 1.42 (0.13), residues: 1488 sheet: -0.12 (0.55), residues: 88 loop : -1.55 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 133 HIS 0.002 0.001 HIS C 421 PHE 0.005 0.001 PHE A 483 TYR 0.014 0.001 TYR D 576 ARG 0.002 0.000 ARG D 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7531 (ptmm) REVERT: D 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7723 (m-80) REVERT: D 454 ASN cc_start: 0.8443 (p0) cc_final: 0.8179 (p0) REVERT: C 118 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7531 (ptmm) REVERT: C 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7724 (m-80) REVERT: C 454 ASN cc_start: 0.8442 (p0) cc_final: 0.8180 (p0) REVERT: B 118 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7530 (ptmm) REVERT: B 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7725 (m-80) REVERT: B 454 ASN cc_start: 0.8442 (p0) cc_final: 0.8180 (p0) REVERT: A 118 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7532 (ptmm) REVERT: A 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7725 (m-80) REVERT: A 454 ASN cc_start: 0.8445 (p0) cc_final: 0.8179 (p0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2905 time to fit residues: 121.8827 Evaluate side-chains 256 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 421 HIS C 421 HIS B 421 HIS A 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17396 Z= 0.289 Angle : 0.550 7.756 23560 Z= 0.282 Chirality : 0.041 0.174 2628 Planarity : 0.004 0.039 2956 Dihedral : 6.825 131.657 2372 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.13 % Allowed : 14.06 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 2116 helix: 1.70 (0.13), residues: 1500 sheet: -0.18 (0.55), residues: 88 loop : -1.45 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.004 0.001 HIS C 421 PHE 0.008 0.001 PHE B 514 TYR 0.013 0.001 TYR B 411 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 1.934 Fit side-chains REVERT: D 108 LYS cc_start: 0.7846 (tptt) cc_final: 0.7505 (tptt) REVERT: D 259 PHE cc_start: 0.8078 (m-80) cc_final: 0.7759 (m-80) REVERT: D 286 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7569 (t-90) REVERT: D 524 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8033 (p) REVERT: D 581 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7835 (tpp80) REVERT: C 108 LYS cc_start: 0.7848 (tptt) cc_final: 0.7506 (tptt) REVERT: C 259 PHE cc_start: 0.8079 (m-80) cc_final: 0.7759 (m-80) REVERT: C 286 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7570 (t-90) REVERT: C 524 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8032 (p) REVERT: C 581 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7836 (tpp80) REVERT: B 108 LYS cc_start: 0.7848 (tptt) cc_final: 0.7507 (tptt) REVERT: B 259 PHE cc_start: 0.8080 (m-80) cc_final: 0.7760 (m-80) REVERT: B 286 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7569 (t-90) REVERT: B 524 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8034 (p) REVERT: B 581 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7836 (tpp80) REVERT: A 108 LYS cc_start: 0.7846 (tptt) cc_final: 0.7521 (tptt) REVERT: A 259 PHE cc_start: 0.8078 (m-80) cc_final: 0.7761 (m-80) REVERT: A 286 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7572 (t-90) REVERT: A 524 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 581 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7837 (tpp80) outliers start: 20 outliers final: 4 residues processed: 268 average time/residue: 0.2894 time to fit residues: 119.3636 Evaluate side-chains 244 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 160 optimal weight: 0.1980 chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17396 Z= 0.161 Angle : 0.490 7.363 23560 Z= 0.247 Chirality : 0.039 0.177 2628 Planarity : 0.003 0.036 2956 Dihedral : 6.849 132.926 2372 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.81 % Allowed : 12.93 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 2116 helix: 2.00 (0.14), residues: 1496 sheet: -0.04 (0.55), residues: 88 loop : -1.39 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 133 HIS 0.002 0.001 HIS C 421 PHE 0.009 0.001 PHE A 514 TYR 0.012 0.001 TYR B 411 ARG 0.001 0.000 ARG D 467 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 2.040 Fit side-chains REVERT: D 259 PHE cc_start: 0.8072 (m-80) cc_final: 0.7736 (m-80) REVERT: D 286 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7546 (t-90) REVERT: D 454 ASN cc_start: 0.8309 (p0) cc_final: 0.7940 (p0) REVERT: D 524 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.7991 (p) REVERT: D 581 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7833 (tpp80) REVERT: C 259 PHE cc_start: 0.8072 (m-80) cc_final: 0.7735 (m-80) REVERT: C 286 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7545 (t-90) REVERT: C 454 ASN cc_start: 0.8305 (p0) cc_final: 0.7938 (p0) REVERT: C 524 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.7991 (p) REVERT: C 581 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7835 (tpp80) REVERT: B 259 PHE cc_start: 0.8073 (m-80) cc_final: 0.7737 (m-80) REVERT: B 286 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7545 (t-90) REVERT: B 454 ASN cc_start: 0.8307 (p0) cc_final: 0.7939 (p0) REVERT: B 524 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.7992 (p) REVERT: B 581 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7833 (tpp80) REVERT: A 259 PHE cc_start: 0.8073 (m-80) cc_final: 0.7739 (m-80) REVERT: A 286 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7547 (t-90) REVERT: A 454 ASN cc_start: 0.8310 (p0) cc_final: 0.7939 (p0) REVERT: A 524 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.7991 (p) REVERT: A 581 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7832 (tpp80) outliers start: 32 outliers final: 9 residues processed: 280 average time/residue: 0.2727 time to fit residues: 118.7428 Evaluate side-chains 265 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17396 Z= 0.205 Angle : 0.494 7.496 23560 Z= 0.251 Chirality : 0.040 0.198 2628 Planarity : 0.003 0.043 2956 Dihedral : 6.809 132.398 2372 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.53 % Allowed : 13.32 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2116 helix: 2.11 (0.14), residues: 1500 sheet: -0.10 (0.55), residues: 88 loop : -1.40 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 281 HIS 0.003 0.001 HIS A 421 PHE 0.010 0.001 PHE D 514 TYR 0.012 0.001 TYR D 411 ARG 0.002 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 2.053 Fit side-chains REVERT: D 113 MET cc_start: 0.8606 (mmm) cc_final: 0.8385 (mmm) REVERT: D 259 PHE cc_start: 0.8085 (m-80) cc_final: 0.7746 (m-80) REVERT: D 286 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7603 (t-90) REVERT: D 454 ASN cc_start: 0.8412 (p0) cc_final: 0.8126 (p0) REVERT: D 523 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7802 (pt) REVERT: D 524 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7923 (p) REVERT: D 581 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7817 (tpp80) REVERT: C 113 MET cc_start: 0.8608 (mmm) cc_final: 0.8388 (mmm) REVERT: C 259 PHE cc_start: 0.8085 (m-80) cc_final: 0.7745 (m-80) REVERT: C 286 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7603 (t-90) REVERT: C 454 ASN cc_start: 0.8408 (p0) cc_final: 0.8125 (p0) REVERT: C 523 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7801 (pt) REVERT: C 524 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.7923 (p) REVERT: C 581 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7818 (tpp80) REVERT: B 113 MET cc_start: 0.8607 (mmm) cc_final: 0.8388 (mmm) REVERT: B 259 PHE cc_start: 0.8087 (m-80) cc_final: 0.7748 (m-80) REVERT: B 286 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7601 (t-90) REVERT: B 454 ASN cc_start: 0.8411 (p0) cc_final: 0.8128 (p0) REVERT: B 523 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7801 (pt) REVERT: B 524 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.7920 (p) REVERT: B 581 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7818 (tpp80) REVERT: A 259 PHE cc_start: 0.8086 (m-80) cc_final: 0.7749 (m-80) REVERT: A 286 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7602 (t-90) REVERT: A 454 ASN cc_start: 0.8408 (p0) cc_final: 0.8123 (p0) REVERT: A 523 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7803 (pt) REVERT: A 524 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 581 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7817 (tpp80) outliers start: 27 outliers final: 11 residues processed: 247 average time/residue: 0.2690 time to fit residues: 104.4970 Evaluate side-chains 254 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 GLN B 124 GLN A 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17396 Z= 0.294 Angle : 0.523 7.738 23560 Z= 0.269 Chirality : 0.041 0.168 2628 Planarity : 0.004 0.049 2956 Dihedral : 6.807 131.567 2372 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 12.70 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2116 helix: 2.03 (0.14), residues: 1496 sheet: 0.10 (0.54), residues: 88 loop : -1.44 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.003 0.001 HIS D 310 PHE 0.011 0.001 PHE B 514 TYR 0.014 0.001 TYR D 411 ARG 0.002 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 2.135 Fit side-chains REVERT: D 113 MET cc_start: 0.8702 (mmm) cc_final: 0.8474 (mmm) REVERT: D 218 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8485 (mp) REVERT: D 259 PHE cc_start: 0.8107 (m-80) cc_final: 0.7774 (m-80) REVERT: D 286 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7757 (t-90) REVERT: D 523 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7730 (pt) REVERT: D 524 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8186 (t) REVERT: D 581 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7895 (tpp80) REVERT: C 113 MET cc_start: 0.8706 (mmm) cc_final: 0.8476 (mmm) REVERT: C 218 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8483 (mp) REVERT: C 259 PHE cc_start: 0.8105 (m-80) cc_final: 0.7773 (m-80) REVERT: C 286 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7759 (t-90) REVERT: C 523 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7730 (pt) REVERT: C 524 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8189 (t) REVERT: C 581 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7894 (tpp80) REVERT: B 113 MET cc_start: 0.8702 (mmm) cc_final: 0.8474 (mmm) REVERT: B 218 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 259 PHE cc_start: 0.8104 (m-80) cc_final: 0.7774 (m-80) REVERT: B 286 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7757 (t-90) REVERT: B 523 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7729 (pt) REVERT: B 524 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8186 (t) REVERT: B 581 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7891 (tpp80) REVERT: A 218 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 259 PHE cc_start: 0.8107 (m-80) cc_final: 0.7777 (m-80) REVERT: A 286 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7706 (t-90) REVERT: A 523 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7730 (pt) REVERT: A 524 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8188 (t) REVERT: A 581 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7892 (tpp80) outliers start: 36 outliers final: 12 residues processed: 251 average time/residue: 0.3094 time to fit residues: 118.7031 Evaluate side-chains 240 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17396 Z= 0.169 Angle : 0.486 7.545 23560 Z= 0.246 Chirality : 0.039 0.160 2628 Planarity : 0.003 0.041 2956 Dihedral : 6.811 132.531 2372 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.15 % Allowed : 13.83 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2116 helix: 2.18 (0.14), residues: 1488 sheet: 0.06 (0.55), residues: 88 loop : -1.36 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 281 HIS 0.003 0.001 HIS A 421 PHE 0.010 0.001 PHE A 514 TYR 0.013 0.001 TYR C 411 ARG 0.007 0.000 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 1.932 Fit side-chains REVERT: D 218 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8341 (mp) REVERT: D 259 PHE cc_start: 0.8080 (m-80) cc_final: 0.7746 (m-80) REVERT: D 286 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7634 (t-90) REVERT: D 454 ASN cc_start: 0.8311 (p0) cc_final: 0.7976 (p0) REVERT: D 523 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7773 (pt) REVERT: D 524 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8192 (t) REVERT: D 581 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7975 (tpp80) REVERT: C 218 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 259 PHE cc_start: 0.8079 (m-80) cc_final: 0.7746 (m-80) REVERT: C 286 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7635 (t-90) REVERT: C 454 ASN cc_start: 0.8306 (p0) cc_final: 0.7973 (p0) REVERT: C 523 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7774 (pt) REVERT: C 524 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8191 (t) REVERT: C 581 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7976 (tpp80) REVERT: B 218 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 259 PHE cc_start: 0.8079 (m-80) cc_final: 0.7747 (m-80) REVERT: B 286 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7634 (t-90) REVERT: B 454 ASN cc_start: 0.8310 (p0) cc_final: 0.7976 (p0) REVERT: B 523 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7773 (pt) REVERT: B 524 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8191 (t) REVERT: B 581 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7974 (tpp80) REVERT: A 113 MET cc_start: 0.8496 (mmm) cc_final: 0.8262 (mmm) REVERT: A 218 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 259 PHE cc_start: 0.8080 (m-80) cc_final: 0.7748 (m-80) REVERT: A 286 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7649 (t-90) REVERT: A 454 ASN cc_start: 0.8308 (p0) cc_final: 0.7973 (p0) REVERT: A 523 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7775 (pt) REVERT: A 524 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 581 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7974 (tpp80) outliers start: 38 outliers final: 15 residues processed: 265 average time/residue: 0.2752 time to fit residues: 113.3674 Evaluate side-chains 262 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17396 Z= 0.173 Angle : 0.502 7.590 23560 Z= 0.252 Chirality : 0.039 0.154 2628 Planarity : 0.003 0.040 2956 Dihedral : 6.805 132.693 2372 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.15 % Allowed : 13.83 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2116 helix: 2.19 (0.14), residues: 1496 sheet: 0.09 (0.54), residues: 88 loop : -1.32 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 281 HIS 0.003 0.001 HIS D 421 PHE 0.010 0.001 PHE D 514 TYR 0.012 0.001 TYR A 411 ARG 0.003 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 1.817 Fit side-chains REVERT: D 218 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8201 (mp) REVERT: D 259 PHE cc_start: 0.8077 (m-80) cc_final: 0.7736 (m-80) REVERT: D 286 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: D 523 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7805 (pt) REVERT: D 524 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8183 (t) REVERT: D 581 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7967 (tpp80) REVERT: C 218 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8199 (mp) REVERT: C 259 PHE cc_start: 0.8075 (m-80) cc_final: 0.7736 (m-80) REVERT: C 286 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: C 523 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7807 (pt) REVERT: C 524 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8182 (t) REVERT: C 540 GLU cc_start: 0.7423 (pm20) cc_final: 0.7100 (pm20) REVERT: C 581 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7970 (tpp80) REVERT: B 218 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8200 (mp) REVERT: B 259 PHE cc_start: 0.8076 (m-80) cc_final: 0.7738 (m-80) REVERT: B 286 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7576 (t-90) REVERT: B 523 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7804 (pt) REVERT: B 524 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8185 (t) REVERT: B 540 GLU cc_start: 0.7423 (pm20) cc_final: 0.7102 (pm20) REVERT: B 581 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7967 (tpp80) REVERT: A 113 MET cc_start: 0.8598 (mmm) cc_final: 0.8348 (mmm) REVERT: A 218 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 259 PHE cc_start: 0.8077 (m-80) cc_final: 0.7739 (m-80) REVERT: A 286 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7635 (t-90) REVERT: A 454 ASN cc_start: 0.8287 (p0) cc_final: 0.7972 (p0) REVERT: A 523 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7809 (pt) REVERT: A 524 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8186 (t) REVERT: A 540 GLU cc_start: 0.7425 (pm20) cc_final: 0.7105 (pm20) REVERT: A 581 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7966 (tpp80) outliers start: 38 outliers final: 15 residues processed: 255 average time/residue: 0.2913 time to fit residues: 116.5925 Evaluate side-chains 260 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17396 Z= 0.183 Angle : 0.507 8.298 23560 Z= 0.253 Chirality : 0.039 0.151 2628 Planarity : 0.003 0.038 2956 Dihedral : 6.786 132.926 2372 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.27 % Allowed : 14.40 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 2116 helix: 2.26 (0.14), residues: 1492 sheet: 0.12 (0.54), residues: 88 loop : -1.34 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.003 0.001 HIS D 421 PHE 0.010 0.001 PHE D 514 TYR 0.012 0.001 TYR A 411 ARG 0.001 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 2.030 Fit side-chains REVERT: D 218 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8211 (mp) REVERT: D 259 PHE cc_start: 0.8073 (m-80) cc_final: 0.7730 (m-80) REVERT: D 286 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7604 (t-90) REVERT: D 523 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7869 (pt) REVERT: D 524 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8188 (t) REVERT: C 218 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8210 (mp) REVERT: C 259 PHE cc_start: 0.8074 (m-80) cc_final: 0.7733 (m-80) REVERT: C 286 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7604 (t-90) REVERT: C 523 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7864 (pt) REVERT: C 524 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8188 (t) REVERT: C 540 GLU cc_start: 0.7438 (pm20) cc_final: 0.7101 (pm20) REVERT: B 218 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 259 PHE cc_start: 0.8075 (m-80) cc_final: 0.7734 (m-80) REVERT: B 286 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7606 (t-90) REVERT: B 523 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7864 (pt) REVERT: B 524 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8188 (t) REVERT: B 540 GLU cc_start: 0.7439 (pm20) cc_final: 0.7102 (pm20) REVERT: A 113 MET cc_start: 0.8520 (mmm) cc_final: 0.8280 (mmm) REVERT: A 218 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8215 (mp) REVERT: A 259 PHE cc_start: 0.8076 (m-80) cc_final: 0.7736 (m-80) REVERT: A 286 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7633 (t-90) REVERT: A 454 ASN cc_start: 0.8282 (p0) cc_final: 0.7976 (p0) REVERT: A 523 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7865 (pt) REVERT: A 524 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8191 (t) REVERT: A 540 GLU cc_start: 0.7441 (pm20) cc_final: 0.7105 (pm20) outliers start: 40 outliers final: 16 residues processed: 257 average time/residue: 0.2455 time to fit residues: 102.1243 Evaluate side-chains 258 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 0.2980 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17396 Z= 0.171 Angle : 0.516 7.953 23560 Z= 0.260 Chirality : 0.039 0.149 2628 Planarity : 0.003 0.038 2956 Dihedral : 6.753 132.444 2372 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.38 % Allowed : 14.29 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 2116 helix: 2.25 (0.14), residues: 1500 sheet: 0.12 (0.54), residues: 88 loop : -1.26 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.003 0.001 HIS A 421 PHE 0.010 0.001 PHE D 514 TYR 0.011 0.001 TYR B 411 ARG 0.001 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 2.047 Fit side-chains REVERT: D 113 MET cc_start: 0.8539 (mmm) cc_final: 0.8315 (mmm) REVERT: D 218 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8382 (mp) REVERT: D 259 PHE cc_start: 0.8070 (m-80) cc_final: 0.7725 (m-80) REVERT: D 286 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7625 (t-90) REVERT: D 523 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7888 (pt) REVERT: D 524 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8195 (t) REVERT: C 113 MET cc_start: 0.8538 (mmm) cc_final: 0.8315 (mmm) REVERT: C 218 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 259 PHE cc_start: 0.8070 (m-80) cc_final: 0.7725 (m-80) REVERT: C 286 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7625 (t-90) REVERT: C 523 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7888 (pt) REVERT: C 524 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8194 (t) REVERT: C 540 GLU cc_start: 0.7430 (pm20) cc_final: 0.7132 (pm20) REVERT: B 113 MET cc_start: 0.8539 (mmm) cc_final: 0.8316 (mmm) REVERT: B 218 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8385 (mp) REVERT: B 259 PHE cc_start: 0.8071 (m-80) cc_final: 0.7729 (m-80) REVERT: B 286 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7625 (t-90) REVERT: B 523 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7889 (pt) REVERT: B 524 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8195 (t) REVERT: B 540 GLU cc_start: 0.7434 (pm20) cc_final: 0.7137 (pm20) REVERT: A 113 MET cc_start: 0.8520 (mmm) cc_final: 0.8143 (tpt) REVERT: A 218 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 259 PHE cc_start: 0.8071 (m-80) cc_final: 0.7729 (m-80) REVERT: A 286 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: A 523 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7890 (pt) REVERT: A 524 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8196 (t) REVERT: A 540 GLU cc_start: 0.7436 (pm20) cc_final: 0.7137 (pm20) outliers start: 42 outliers final: 16 residues processed: 259 average time/residue: 0.2493 time to fit residues: 103.2673 Evaluate side-chains 260 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 0.0170 chunk 95 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17396 Z= 0.164 Angle : 0.522 7.840 23560 Z= 0.263 Chirality : 0.039 0.152 2628 Planarity : 0.003 0.037 2956 Dihedral : 6.781 132.955 2372 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.87 % Allowed : 14.91 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 2116 helix: 2.27 (0.14), residues: 1496 sheet: 0.14 (0.54), residues: 88 loop : -1.31 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.003 0.001 HIS D 421 PHE 0.010 0.001 PHE A 514 TYR 0.011 0.001 TYR B 411 ARG 0.003 0.000 ARG A 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 2.082 Fit side-chains REVERT: D 218 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8348 (mp) REVERT: D 259 PHE cc_start: 0.8067 (m-80) cc_final: 0.7721 (m-80) REVERT: D 286 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7638 (t-90) REVERT: D 523 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7895 (pt) REVERT: D 524 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8194 (t) REVERT: C 218 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8347 (mp) REVERT: C 259 PHE cc_start: 0.8067 (m-80) cc_final: 0.7722 (m-80) REVERT: C 286 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7635 (t-90) REVERT: C 523 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7931 (pt) REVERT: C 524 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8192 (t) REVERT: C 540 GLU cc_start: 0.7421 (pm20) cc_final: 0.7125 (pm20) REVERT: B 218 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8350 (mp) REVERT: B 259 PHE cc_start: 0.8069 (m-80) cc_final: 0.7725 (m-80) REVERT: B 286 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7636 (t-90) REVERT: B 523 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7932 (pt) REVERT: B 524 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8194 (t) REVERT: B 540 GLU cc_start: 0.7418 (pm20) cc_final: 0.7124 (pm20) REVERT: A 113 MET cc_start: 0.8479 (mmm) cc_final: 0.8111 (tpt) REVERT: A 218 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8349 (mp) REVERT: A 259 PHE cc_start: 0.8069 (m-80) cc_final: 0.7725 (m-80) REVERT: A 286 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7638 (t-90) REVERT: A 523 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7897 (pt) REVERT: A 524 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8196 (t) REVERT: A 540 GLU cc_start: 0.7422 (pm20) cc_final: 0.7126 (pm20) outliers start: 33 outliers final: 16 residues processed: 255 average time/residue: 0.2572 time to fit residues: 103.8162 Evaluate side-chains 265 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117764 restraints weight = 19907.716| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.30 r_work: 0.3315 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17396 Z= 0.213 Angle : 0.546 8.060 23560 Z= 0.273 Chirality : 0.040 0.146 2628 Planarity : 0.003 0.042 2956 Dihedral : 6.779 132.454 2372 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.04 % Allowed : 14.97 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2116 helix: 2.24 (0.14), residues: 1492 sheet: 0.20 (0.54), residues: 88 loop : -1.35 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 133 HIS 0.003 0.001 HIS B 421 PHE 0.011 0.001 PHE D 514 TYR 0.012 0.001 TYR D 411 ARG 0.004 0.000 ARG A 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3658.22 seconds wall clock time: 67 minutes 22.37 seconds (4042.37 seconds total)